What’s the Answer? (publishing tool papers)

Biostars is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the Biostars_logo community and find it very useful. Often questions and answers arise at Biostars that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those items or discussions here in this thread. You can ask questions in this thread, or you can always join in at Biostars.

This week’s highlighted forum discussion was really interesting to me. In the original post, there are pros and cons of publishing software tool papers. I think all of these are useful points for discussion. But it was also interesting what others commented and replied on the topic.

Forum: On the utility of publishing a tool paper

I’ve been considering writing an application note for the pyfaidx module (for reading/writing indexed FASTA files), but I’m not sure if the effort involved in authoring and publishing an application note is worth it. Several projects have published their work as application notes, but I’m not sure that a “me too” attitude helps here.

Reasons I can think of for publishing a tool:

  1. Citations. Obviously it’s easier for people to reference your work.
  2. Content discovery. Not everyone knows what they’re searching for, and while GitHub and Google do help here, not everyone is an SEO genius.
  3. Context for usage. Several application notes I’ve seen provide use cases or examples where the tool may provide an advantage.


  1. Time
  2. Publication fees
  3. Danger of producing a stale description of your software. Software development should be motivated by use cases, bugs, and user feedback. All can really change the functionality and interface of software.

Any thoughts about pros/cons of tool publications would help.

Matt Shirley

Go have a look at the discussion in full. A someone who has searched for a lot of software, only to find references to internal personal scripts, broken links and outdated personal web pages in too many cases, I certainly favor publishing in some findable, archived format somewhere. But I don’t think it has to cost much–I don’t care if it was in a traditional journal format. There are ways around that now that would perfectly suffice for these types of smaller utilities or data sets.